New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
17 months
30
19
74022
7788
Parser of scientific names (...) !
Dmitry Mozzherin
11 weeks
16
5
39540
2832
0
7
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
6 months
5
1
33515
3555
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
5 months
14
11
32045
1889
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
1 week
17
5
27017
2179
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
4 weeks
2
...
23296
3139
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
7 months
13
1
20368
1421
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
20113
1055
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
16 months
...
18610
1804
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
7 months
...
17419
2885
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
9 months
30
22
16798
1078
0
159
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
16028
842
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
14480
1038
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
13593
697
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
9 months
9
5
12783
1344
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
24 months
5
...
12426
987
A simple obo file handler (...) !
mjy
3 years
4
...
12043
513
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
11968
835
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
6 weeks
11
...
10267
1225
0
57
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
9285
605
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
5 months
6
5
8986
606
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
4 months
7
20
8512
780
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
8002
431
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
20 months
1
...
7829
505
0
13
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
7813
294
Low memory sequence emitters (...)
Pjotr Prins
5 months
8
1
7401
505
0
0
Build genome output files (...)
Michael Barton
14 months
3
...
7335
336
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
7067
342
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7010
297
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
11 weeks
1
...
6820
596
Data mining algorithms for jRuby (...)
arrigonialberto86
13 months
14
3
6732
891
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
14 months
8
2
6606
652
10
28
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
23 months
2
...
6558
432
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
6552
333
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
16 months
8
...
6504
351
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6384
232
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6352
349
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6227
424
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
6084
265
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
17 months
5
...
6077
503
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5879
288
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5662
290
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5394
249
Ruby support for the baclava file format (...) !
Robert Haines
7 months
1
...
5309
2280
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
9
...
4700
185
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4695
276
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4680
344
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4490
262
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
4
4434
158
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
23 months
2
...
4302
250
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
18 months
2
1
4046
335
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
7 months
...
3981
2428
0
0
Ruby binding for samtools tabix (...)
throwern
12 months
3
...
3771
368
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
14 months
11
2
3764
773
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3610
177
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3576
167
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3476
252
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3409
251
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3406
264
Next-generation mapping of mutations (...)
Dan MacLean
22 months
2
...
3394
261
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3309
189
3
42
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3265
194
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3054
162
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
5 weeks
4
3
2909
576
0
25
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2880
170
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2826
167
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
20 months
...
2628
245
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
13 months
...
2541
334
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
17 months
...
2506
241
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2494
174
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
14 months
1
...
2481
258
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
1 week
1
...
2465
1486
A protparam compatible utility for BioRuby (...)
hryk
22 months
1
...
2438
175
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
23 months
2
...
2338
169
Parser to work with file formats used in (...)
Ben J Woodcroft
3 months
...
2021
560
Publish scientific results to the semantic web (...) !
Will Strinz
4 months
3
16
1926
260
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1885
96
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1862
88
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1860
88
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1798
75
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
5 weeks
12
8
1719
711
3
53
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
8 months
6
...
1674
101
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1609
92
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1604
89
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1570
95
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1560
96
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1553
93
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1533
89
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
4
...
1514
97
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1498
93
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1480
86
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1466
92
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1453
93
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
19 months
1
...
1406
97
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
7 months
1
...
1385
344
Gggenome Ruby client (...)
Mitsuteru Nakao
14 months
1
...
1364
169
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1346
98
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1291
60
Ruby ensembl rest api (...)
Alberto Donizetti
13 months
3
1
1278
176
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1255
95
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1252
94
Generalized linear models for statsample (...)
Ankur Goel
13 months
...
1226
169
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
1 week
...
1052
824
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
21 months
...
1000
87
Biostars data-mining and statistical analysis (...)
Joachim Baran
6 months
...
984
282
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
9 months
...
961
186
Interface for express beta diversity (...)
Ben J. Woodcroft
9 months
...
931
183
Bio-repeatmasker (...)
Andrei Rozanski
9 months
923
185
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
16 months
2
...
789
95
A parser for cigar format alignments (...)
Ben J Woodcroft
7 months
4
...
772
180
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
15 months
...
726
98
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
5 months
1
680
186
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
646
646
0
0
Web server for bio-samtools (...)
homonecloco
4 months
...
626
198
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
2 weeks
...
394
212
Mine publications for gene names (...)
Pjotr Prins
7 months
...
387
92
0
0
(...) pre
pre
366
15
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
3 weeks
...
342
342
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
5 years
30
1
322
322
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
7 months
2
...
312
70
0
0
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
3 months
...
224
128
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
5 years
168
168
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
4 weeks
...
135
70
!
Tools to manipulate blat files from the command (...) new
homonecloco
3 weeks
...
127
127
!
Tools to work with fasta files, indexed with (...) new
homonecloco
2 weeks
...
122
122
(...) pre
pre
98
18
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-10-24
**) number of commits on GitHub (last 7 days & last 90 days)